A review on the impact of single-stranded library preparation on plasma cell-free diversity for cancer detection

Jordan C Cheng; Neeti Swarup; David T W Wong; David Chia

doi:10.3389/fonc.2024.1332004

A review on the impact of single-stranded library preparation on plasma cell-free diversity for cancer detection

Front Oncol. 2024 Mar 6:14:1332004. doi: 10.3389/fonc.2024.1332004. eCollection 2024.

Authors

Jordan C Cheng^{1

2}, Neeti Swarup¹, David T W Wong¹, David Chia³

Affiliations

¹ School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States.
² Stanford Cancer Institute, Stanford University, Stanford, CA, United States.
³ Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.

Abstract

In clinical oncology, cell-free DNA (cfDNA) has shown immense potential in its ability to noninvasively detect cancer at various stages and monitor the progression of therapy. Despite the rapid improvements in cfDNA liquid biopsy approaches, achieving the required sensitivity to detect rare tumor-derived cfDNA still remains a challenge. For next-generation sequencing, the perceived presentation of cfDNA is strongly linked to the extraction and library preparation protocols. Conventional double-stranded DNA library preparation (dsDNA-LP) focuses on assessing ~167bp double-stranded mononucleosomal (mncfDNA) and its other oligonucleosomal cell-free DNA counterparts in plasma. However, dsDNA-LP methods fail to include short, single-stranded, or nicked DNA in the final library preparation, biasing the representation of the actual cfDNA populations in plasma. The emergence of single-stranded library preparation (ssDNA-LP) strategies over the past decade has now allowed these other populations of cfDNA to be studied from plasma. With the use of ssDNA-LP, single-stranded, nicked, and ultrashort cfDNA can be comprehensively assessed for its molecular characteristics and clinical potential. In this review, we overview the current literature on applications of ssDNA-LP on plasma cfDNA from a potential cancer liquid biopsy perspective. To this end, we discuss the molecular principles of single-stranded DNA adapter ligation, how library preparation contributes to the understanding of native cfDNA characteristics, and the potential for ssDNA-LP to improve the sensitivity of circulating tumor DNA detection. Additionally, we review the current literature on the newly reported species of plasma ultrashort single-stranded cell-free DNA plasma, which appear biologically distinct from mncfDNA. We conclude with a discussion of future perspectives of ssDNA-LP for liquid biopsy endeavors.

Keywords: cell-free DNA; fragment-size; liquid biopsy; single-stranded library preparation; ultrashort single-stranded cell-free DNA.

Publication types

Review

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by NCI K00CA264398-03 to JC, NIH grants 2U01CA233370-06 to DW and 1R90DE031531 to NS.